RetrogeneDB ID: retro_etel_2096

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_55150:79..612(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000008154
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VIMP
• Ensembl ID: ENSETEG00000011401
• Aliases: None
• Description: VCP-interacting membrane protein [Source:HGNC Symbol;Acc:30396]

Sequence

>retro_etel_2096
CGAGCATCTCTGGAAACGGAGGGGTTGCGCTTCTTGCATGTCACAGTGGGTTCCCTGCTGGTCGCCTATGGCTGGTACAT
CATCTTCAGCTGTGTCCTTTTCCTGTGGTCACTCAGAAGCTCTCTGCCCGACTTAGGGCTTTGAGGCAGAGGCAGCTGGA
CCAAGAAACAACTGCTGTGGAACCTGCTGTGATTGTTAAATGACAAGAAGCTTTAGCAGCCGCTCGTTGAAAAATGCAAG
AAGAATTAAATGCTCAAGCTGAAAAGCATAAAGAAGAACTGAGAGAGCTGGAAGAAGAGAAAAGGAGACTGAAGACTGTC
AAGGGGGACAGCATGCCAGAAGGAAAAAGCTACAAAGGAAATGTCAAAAGGCCTCAGGAAGAAGACAGCTCTGCGCCTTC
CACATCATCAGTTCCCCCCAAACGTACGCCTGAGAGAAAGCCATTGCGCCGAGGTGGTTCCAACCCTCTGTCTGGGGAAG
GAGGTGGCACATGCTCCTGGACACCTGGGCGAAGAGGTCCATCCTCTGGCGGA

Alignment

ORF - retro_etel_2096 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.54 %
• Parental protein coverage: 94.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RPALETEGLRFLHVTVGSLLATYGWYIIFSCILLL-VVIQKLSARFRALRQRQLDQETTVVEPDIIVKRQ
          R..LETEGLRFLHVTVGSLL..YGWYIIFSC.L.L.VV.QKLSAR.RALRQRQLDQETT.VEP..IVK.Q
Retrocopy RASLETEGLRFLHVTVGSLLVAYGWYIIFSCVLFL<VVTQKLSARLRALRQRQLDQETTAVEPAVIVK*Q

Parental  EALAAARLKMQEELNAQAEKHKEKLRQXXXXXXXXXXXXXXXMQEGK-YKGSVRRPHEEDHSVPSTSSVP
          EALAAAR.KMQEELNAQAEKHKE.LR................M.EGK.YKG.V.RP.EED.S.PSTSSVP
Retrocopy EALAAAR*KMQEELNAQAEKHKEELRELEEEKRRLKTVKGDSMPEGKSYKGNVKRPQEEDSSAPSTSSVP

Parental  PKHKPERKPLRRGGYNPLSGEGGGTCSWRPGRRGPSSGG
          PK..PERKPLRRGG.NPLSGEGGGTCSW.PGRRGPSSGG
Retrocopy PKRTPERKPLRRGGSNPLSGEGGGTCSWTPGRRGPSSGG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_2096 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007115	1 retrocopy	retro_amel_177,
Bos taurus	ENSBTAG00000000640	1 retrocopy	retro_btau_1044,
Dasypus novemcinctus	ENSDNOG00000010694	2 retrocopies	retro_dnov_207, retro_dnov_880,
Echinops telfairi	ENSETEG00000011401	1 retrocopy	retro_etel_2096 ,
Felis catus	ENSFCAG00000028822	1 retrocopy	retro_fcat_1524,
Pteropus vampyrus	ENSPVAG00000012873	1 retrocopy	retro_pvam_1334,